A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover

Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant expansion. Here, we demonstrate a solution by engineering a synthetic differentiation circuit in Escherichia coli that selects against these mutants via a biphasic fitness strategy. The circuit provides tunable production of synthetic analogs of stem, progenitor, and differentiated cells. It resists mutations by coupling differentiation to the production of an essential enzyme, thereby disadvantaging non-differentiating mutants. The circuit selected for and maintained a positive differentiation rate in long-term evolution. Surprisingly, this rate remained constant across vast changes in growth conditions. We found that transit-amplifying cells (fast-growing progenitors) underlie this environmental robustness. Our results provide insight into the stability of differentiation and demonstrate a powerful method for engineering evolutionarily stable multicellular consortia.

Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing

Antibiotic effectiveness depends on a variety of factors. While many mechanistic details of antibiotic action are known, the connection between death rate and bacterial physiology is poorly understood. A common observation is that death rate in antibiotics rises linearly with growth rate; however, it remains unclear how other factors, such as environmental conditions and whole-cell physiological properties, affect bactericidal activity. To address this, we developed a high-throughput assay to precisely measure antibiotic-mediated death. We found that death rate is linear in growth rate, but the slope depends on environmental conditions. Growth under stress lowers death rate compared to nonstressed environments with similar growth rate. To understand stress's role, we developed a mathematical model of bacterial death based on resource allocation that includes a stress-response sector; we identify this sector using RNA-seq. Our model accurately predicts the minimal inhibitory concentration (MIC) with zero free parameters across a wide range of growth conditions. The model also quantitatively predicts death and MIC when sectors are experimentally modulated using cyclic adenosine monophosphate (cAMP), including protection from death at very low cAMP levels. The present study shows that different conditions with equal growth rate can have different death rates and establishes a quantitative relation between growth, death, and MIC that suggests approaches to improve antibiotic efficacy.

Timescales of Human Hair Cortisol Dynamics

Cortisol is a major human stress hormone, secreted within minutes of acute stress. Cortisol also has slower patterns of variation: a strong circadian rhythm and a seasonal rhythm. However, longitudinal cortisol dynamics in healthy individuals over timescales of months has rarely been studied. Here, we measured longitudinal cortisol in 55 healthy participants using 12 cm of hair, which provides a retrospective measurement over one year. Individuals showed (non-seasonal) fluctuations averaging about 22% around their baseline. Fourier analysis reveals dominant slow frequencies with periods of months to a year. These frequencies can be explained by a mathematical model of the hormonal cascade that controls cortisol, the HPA axis, when including the slow timescales of tissue turnover of the glands. Measuring these dynamics is important for understanding disorders in which cortisol secretion is impaired over months, such as mood disorders, and to test models of cortisol feedback control.

A Bacterial Growth Law out of Steady State

Bacterial growth follows simple laws in constant conditions. However, bacteria in nature often face fluctuating environments. We therefore ask whether there are growth laws that apply to changing environments. We derive a law for upshifts using an optimal resource-allocation model: the post-shift growth rate equals the geometrical mean of the pre-shift growth rate and the growth rate on saturating carbon. We test this using chemostat and batch culture experiments, as well as previous data from several species. The increase in growth rate after an upshift indicates that ribosomes have spare capacity (SC). We demonstrate theoretically that SC has the cost of slow steady-state growth but is beneficial after an upshift because it prevents large overshoots in intracellular metabolites and allows rapid response to change. We also provide predictions for downshifts. The present study quantifies the optimal degree of SC, which rises the slower the growth rate, and suggests that SC can be precisely regulated.

Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP

In most conditions, glucose is the best carbon source for E. coli: it provides faster growth than other sugars, and is consumed first in sugar mixtures. Here we identify conditions in which E. coli strains grow slower on glucose than on other sugars, namely when a single amino acid (arginine, glutamate, or proline) is the sole nitrogen source. In sugar mixtures with these nitrogen sources, E. coli still consumes glucose first, but grows faster rather than slower after exhausting glucose, generating a reversed diauxic shift. We trace this counterintuitive behavior to a metabolic imbalance: levels of TCA-cycle metabolites including α-ketoglutarate are high, and levels of the key regulatory molecule cAMP are low. Growth rates were increased by experimentally increasing cAMP levels, either by adding external cAMP, by genetically perturbing the cAMP circuit or by inhibition of glucose uptake. Thus, the cAMP control circuitry seems to have a ‘bug’ that leads to slow growth under what may be an environmentally rare condition.

Hierarchy of non-glucose sugars in Escherichia coli

BACKGROUND

Understanding how cells make decisions, and why they make the decisions they make, is of fundamental interest in systems biology. To address this, we study the decisions made by E. coli on which genes to express when presented with two different sugars. It is well-known that glucose, E. coli's preferred carbon source, represses the uptake of other sugars by means of global and gene-specific mechanisms. However, less is known about the utilization of glucose-free sugar mixtures which are found in the natural environment of E. coli and in biotechnology.

RESULTS

Here, we combine experiment and theory to map the choices of E. coli among 6 different non-glucose carbon sources. We used robotic assays and fluorescence reporter strains to make precise measurements of promoter activity and growth rate in all pairs of these sugars. We find that the sugars can be ranked in a hierarchy: in a mixture of a higher and a lower sugar, the lower sugar system shows reduced promoter activity. The hierarchy corresponds to the growth rate supported by each sugar- the faster the growth rate, the higher the sugar on the hierarchy. The hierarchy is 'soft' in the sense that the lower sugar promoters are not completely repressed. Measurement of the activity of the master regulator CRP-cAMP shows that the hierarchy can be quantitatively explained based on differential activation of the promoters by CRP-cAMP. Comparing sugar system activation as a function of time in sugar pair mixtures at sub-saturating concentrations, we find cases of sequential activation, and also cases of simultaneous expression of both systems. Such simultaneous expression is not predicted by simple models of growth rate optimization, which predict only sequential activation. We extend these models by suggesting multi-objective optimization for both growing rapidly now and preparing the cell for future growth on the poorer sugar.

CONCLUSION

We find a defined hierarchy of sugar utilization, which can be quantitatively explained by differential activation by the master regulator cAMP-CRP. The present approach can be used to understand cell decisions when presented with mixtures of conditions.

Linear superposition and prediction of bacterial promoter activity dynamics in complex conditions

Bacteria often face complex environments. We asked how gene expression in complex conditions relates to expression in simpler conditions. To address this, we obtained accurate promoter activity dynamical measurements on 94 genes in E. coli in environments made up of all possible combinations of four nutrients and stresses. We find that the dynamics across conditions is well described by two principal component curves specific to each promoter. As a result, the promoter activity dynamics in a combination of conditions is a weighted average of the dynamics in each condition alone. The weights tend to sum up to approximately one. This weighted-average property, called linear superposition, allows predicting the promoter activity dynamics in a combination of conditions based on measurements of pairs of conditions. If these findings apply more generally, they can vastly reduce the number of experiments needed to understand how E. coli responds to the combinatorially huge space of possible environments.

Bacteria face complex conditions in important settings such as our body and in biotechnological applications such as biofuel production. Understanding how bacteria respond to complex conditions is a hard problem: the number of conditions that need to be tested grows exponentially with the number of nutrients, stresses and other factors that make up the environment. To overcome this exponential explosion, we present an approach that allows computing the dynamics of gene expression in a complex condition based on measurements in simple conditions. This is based on the main discovery in this paper: using accurate promoter activity measurements, we find that promoter activity dynamics in a cocktail of media is a weighted average of the dynamics in each medium alone. The weights in the average are constant across time, and can be used to predict the dynamics in arbitrary cocktails based only on measurements on pairs of conditions. Thus, dynamics in complex conditions is, for the vast majority of genes, much simpler than it might have been; this simplicity allows new mathematical formula for accurate prediction in new conditions.

Promoter activity dynamics in the lag phase of Escherichia coli

Background

Lag phase is a period of time with no growth that occurs when stationary phase bacteria are transferred to a fresh medium. Bacteria in lag phase seem inert: their biomass does not increase. The low number of cells and low metabolic activity make it difficult to study this phase. As a consequence, it has not been studied as thoroughly as other bacterial growth phases. However, lag phase has important implications for bacterial infections and food safety. We asked which, if any, genes are expressed in the lag phase of Escherichia coli, and what is their dynamic expression pattern.

Results

We developed an assay based on imaging flow cytometry of fluorescent reporter cells that overcomes the challenges inherent in studying lag phase. We distinguish between lag1 phase- in which there is no biomass growth, and lag2 phase- in which there is biomass growth but no cell division. We find that in lag1 phase, most promoters are not active, except for the enzymes that utilize the specific carbon source in the medium. These genes show promoter activities that increase exponentially with time, despite the fact that the cells do not measurably increase in size. An oxidative stress promoter, katG, is also active. When cells enter lag2 and begin to grow in size, they switch to a full growth program of promoter activity including ribosomal and metabolic genes.

Conclusions

The observed exponential increase in enzymes for the specific carbon source followed by an abrupt switch to production of general growth genes is a solution of an optimal control model, known as bang-bang control. The present approach contributes to the understanding of lag phase, the least studied of bacterial growth phases.

Promoters maintain their relative activity levels under different growth conditions

Most genes change expression levels across conditions, but it is unclear which of these changes represents specific regulation and what determines their quantitative degree. Here, we accurately measured activities of ~900 S. cerevisiae and ~1800 E. coli promoters using fluorescent reporters. We show that in both organisms 60-90% of promoters change their expression between conditions by a constant global scaling factor that depends only on the conditions and not on the promoter's identity. Quantifying such global effects allows precise characterization of specific regulation-promoters deviating from the global scale line. These are organized into few functionally related groups that also adhere to scale lines and preserve their relative activities across conditions. Thus, only several scaling factors suffice to accurately describe genome-wide expression profiles across conditions. We present a parameter-free passive resource allocation model that quantitatively accounts for the global scaling factors. It suggests that many changes in expression across conditions result from global effects and not specific regulation, and provides means for quantitative interpretation of expression profiles.

The last generation of bacterial growth in limiting nutrient

Background

Bacterial growth as a function of nutrients has been studied for decades, but is still not fully understood. In particular, the growth laws under dynamically changing environments have been difficult to explore, because of the rapidly changing conditions. Here, we address this challenge by means of a robotic assay and measure bacterial growth rate, promoter activity and substrate level at high temporal resolution across the entire growth curve in batch culture. As a model system, we study E. coli growing under nitrogen or carbon limitation, and explore the dynamics in the last generation of growth where nutrient levels can drop rapidly.

Results

We find that growth stops abruptly under limiting nitrogen or carbon, but slows gradually when nutrients are not limiting. By measuring growth rate at a 3 min time resolution, and inferring the instantaneous substrate level, s, we find that the reduction in growth rate μ under nutrient limitation follows Monod’s law, μ=μ0sks+s. By following promoter activity of different genes we found that the abrupt stop of growth under nitrogen or carbon limitation is accompanied by a pulse-like up-regulation of the expression of genes in the relevant nutrient assimilation pathways. We further find that sharp stop of growth is conditional on the presence of regulatory proteins in the assimilation pathway.

Conclusions

The observed sharp stop of growth accompanied by a pulsed expression of assimilation genes allows bacteria to compensate for the drop in nutrients, suggesting a strategy used by the cells to prolong exponential growth under limiting substrate.

Mode of regulation and the insulation of bacterial gene expression

A gene can be said to be insulated from environmental variations if its expression level depends only on its cognate inducers, and not on variations in conditions. We tested the insulation of the lac promoter of E. coli and of synthetic constructs in which the transcription factor CRP acts as either an activator or a repressor, by measuring their input function-their expression as a function of inducers-in different growth conditions. We find that the promoter activities show sizable variation across conditions of 10%-100% (SD/mean). When the promoter is bound to its cognate regulator(s), variation across conditions is smaller than when it is unbound. Thus, mode of regulation affects insulation: activators seem to show better insulation at high expression levels, and repressors at low expression levels. This may explain the Savageau demand rule, in which E. coli genes needed often in the natural environment tend to be regulated by activators, and rarely needed genes by repressors. The present approach can be used to study insulation in other genes and organisms.

A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alone.

Many biological processes in a cell involve small numbers of molecules and therefore fluctuate over time. As a consequence, genetically identical cells that live in the same environment differ from each other in many phenotypic traits, including the expression level of different genes. Our aim was to identify types of genes with particularly low or high levels of variation (“noise”) and to understand molecular and evolutionary factors that determine noise level. Working with the bacterium E. coli, we analyzed the expression—at the single cell level—of more than 1,500 different genes. We found particularly low levels of noise in genes that E. coli needs to live and genes that this bacterium shares with many related taxa. This suggests that cellular functions that are particularly important for this organism evolved towards low levels of variation. In contrast to previous results with yeast, we find that genes that change their expression levels in response to environmental signals do not have high levels of noise. This suggests that there may be fundamental differences in how noise is controlled in bacteria and eukaryotes.

Robust control of nitrogen assimilation by a bifunctional enzyme in E. coli

Bacteria regulate the assimilation of multiple nutrients to enable growth. How is balanced utilization achieved, despite fluctuations in the concentrations of the enzymes that make up the regulatory circuitry? Here we address this question by studying the nitrogen system of E. coli. A mechanism based on the avidity of a bifunctional enzyme, adenylyltransferase (AT/AR), to its multimeric substrate, glutamine synthetase, is proposed to maintain a robust ratio between two key metabolites, glutamine and α-ketoglutarate. This ratio is predicted to be insensitive to variations in protein levels of the core circuit and to the rate of nitrogen utilization. We find using mass spectrometry that the metabolite ratio is robust to variations in protein levels and that this robustness depends on the bifunctional enzyme. Moreover, robustness carries through to the bacteria growth rate. Interrupting avidity by adding a monofunctional AT/AR mutant to the native system abolishes robustness, as predicted by the proposed mechanism.

Invariant distribution of promoter activities in Escherichia coli

Cells need to allocate their limited resources to express a wide range of genes. To understand how Escherichia coli partitions its transcriptional resources between its different promoters, we employ a robotic assay using a comprehensive reporter strain library for E. coli to measure promoter activity on a genomic scale at high-temporal resolution and accuracy. This allows continuous tracking of promoter activity as cells change their growth rate from exponential to stationary phase in different media. We find a heavy-tailed distribution of promoter activities, with promoter activities spanning several orders of magnitude. While the shape of the distribution is almost completely independent of the growth conditions, the identity of the promoters expressed at different levels does depend on them. Translation machinery genes, however, keep the same relative expression levels in the distribution across conditions, and their fractional promoter activity tracks growth rate tightly. We present a simple optimization model for resource allocation which suggests that the observed invariant distributions might maximize growth rate. These invariant features of the distribution of promoter activities may suggest design constraints that shape the allocation of transcriptional resources.

Cells respond to a changing environment by regulating the activity of genes. Here, we sought to understand how E. coli cells distribute their limited transcriptional resources among their target genes, and how this allocation varies with growth rate and growth conditions. To achieve this, we assayed the expression of a comprehensive library of transcriptional reporter strains under different conditions. High-temporal resolution measurements of promoter activities were obtained for different growth rates spanning recovery from stationary phase into exponential phase and eventually deep stationary phase again. We find that the genome-wide promoter activity follows a power-law distribution, which depends solely on growth rate and is independent of the specific growth conditions. Moreover, we find that the power-law distribution can be decomposed into two log-normal distributions: metabolic promoters that make up the low end of the distribution, and ribosomal promoters that make up the high end of the distribution. While distributions remained constant for a given growth rate, the ranked expression of metabolic promoters differed according to the specific condition. Thus, the invariant distribution may suggest optimal resource allocation under constrained resources. A mathematical theory is presented to explain these results.

The incoherent feed-forward loop can generate non-monotonic input functions for genes

Gene regulation networks contain recurring circuit patterns called network motifs. One of the most common network motif is the incoherent type 1 feed-forward loop (I1-FFL), in which an activator controls both gene and repressor of that gene. This motif was shown to act as a pulse generator and response accelerator of gene expression. Here we consider an additional function of this motif: the I1-FFL can generate a non-monotonic dependence of gene expression on the input signal. Here, we study this experimentally in the galactose system of Escherichia coli, which is regulated by an I1-FFL. The promoter activity of two of the gal operons, galETK and galP, peaks at intermediate levels of the signal cAMP. We find that mutants in which the I1-FFL is disrupted lose this non-monotonic behavior, and instead display monotonic input functions. Theoretical analysis suggests that non-monotonic input functions can be achieved for a wide range of parameters by the I1-FFL. The models also suggest regimes where a monotonic input-function can occur, as observed in the mglBAC operon regulated by the same I1-FFL. The present study thus experimentally demonstrates how upstream circuitry can affect gene input functions and how an I1-FFL functions within its natural context in the cell.

A comprehensive library of fluorescent transcriptional reporters for Escherichia coli

E. coli is widely used for systems biology research; there exists a need, however, for tools that can be used to accurately and comprehensively measure expression dynamics in individual living cells. To address this we present a library of transcriptional fusions of gfp to each of about 2,000 different promoters in E. coli K12, covering the great majority of the promoters in the organism. Each promoter fusion is expressed from a low-copy plasmid. We demonstrate that this library can be used to obtain highly accurate dynamic measurements of promoter activity on a genomic scale, in a glucose-lactose diauxic shift experiment. The library allowed detection of about 80 previously uncharacterized transcription units in E. coli, including putative internal promoters within previously known operons, such as the lac operon. This library can serve as a tool for accurate, high-resolution analysis of transcription networks in living E. coli cells.

Follow-up of Kidney Graft Recipients With Cyclosporine-Associated Hemolytic-Uremic Syndrome and Thrombotic Microangiopathy

The study was based on 462 patients who underwent kidney transplantation from 1986 through 2004. Cyclosporine (CsA)-related thrombotic microangiopathy (TMA) was observed in 15 (3.3%) patients. The donor ages ranged from 9 to 51 years and cold ischemia times from 12 to 31 hours. Hemolytic-uremic syndrome (HUS) developed 2 weeks after transplantation in 14 patients and later in 1 subject. Histopathologic examination demonstrated glomerular-type TMA in 3 patients, a mixed type (glomerular and vascular) in 11 patients, and a nonspecific mesangial widening with tubulointerstitial lesions in 1 patient. Follow-up biopsies revealed resolution of TMA in 4 patients and chronic vascular TMA in 1 patient. Six patients with mixed-type TMA needed transient hemodialysis. No patient with the glomerular-type TMA needed dialysis (P = .103), and 14 of 15 had good resolution of graft function after CsA dose reduction or temporary discontinuation or continuation of optimal dose. Only 1 graft with mixed-type TMA was lost due to irreversible HUS. The mean glomerular filtration rate (GFR), predicted by the Nankivell equation, was 76 +/- 13 mL/min and 80 +/- 27 mL/min at 1 month after discharge for glomerular- and mixed-type TMA, respectively (P > .05). GFRs 1 year after HUS were 82 +/- 12 and 87 +/- 21 mL/min for the glomerular and the mixed types, respectively (P > .05). We concluded that the mixed-type TMA was associated with a more severe early clinical course than the glomerular-type TMA. The 1-year prognosis was good in the majority of patients, with no significant differences between those with the glomerular- and mixed-type TMA.

Changing the direction of flagellar rotation in bacteria by modulating the ratio between the rotational states of the switch protein FliM

One of the major questions in bacterial chemotaxis is how the switch, which controls the direction of flagellar rotation, functions. It is well established that binding of the signaling molecule CheY to the switch protein FliM shifts the rotation from the default direction, counterclockwise, to clockwise. How this shift is done is still a mystery. Our aim in this study was to determine the correlation between the fraction of FliM molecules in the clockwise state (i.e. occupied by CheY) and the probability of clockwise rotation. For this purpose we gradually expressed, from a plasmid, a clockwise FliM mutant protein in cells that express, from the chromosome, wild-type FliM but no chemotaxis proteins. We verified that plasmid-borne FliM exchanges chromosomal FliM in the switch. Surprisingly, a substantial clockwise probability was not obtained before the large majority of the FliM molecules in the switch were clockwise molecules. Thereafter, the rise in clockwise probability was very steep. These results suggest that an increase in the clockwise probability requires a high level of FliM occupancy by CheY approximately P. They further suggest that the steep increase in clockwise rotation upon increasing CheY levels, reported in several studies, is due, at least in part, to cooperativity of post-binding interactions within the switch. We also carried out the inverse experiment, in which wild-type FliM was gradually expressed in a background of a clockwise fliM mutant. In this case, the level of the clockwise mutant protein, required for establishing a certain clockwise probability, was lower than in the original experiment. If our system (in which the ratio between the rotational states of FliM in the switch is established by slow exchange) and the native system (in which the ratio is established by fast changes in FliM occupancy) are comparable, the results suggest that hysteresis is involved in the switch function. Such a situation might reflect a damping mechanism, which prevents a situation in which fluctuations in the phosphorylation level of CheY throw the switch from one direction of rotation to the other.

Bone histomorphometry is still the golden standard for diagnosing renal osteodystrophy

AIM

The clinical picture of renal osteodystrophy (RO) is very uncharacteristic. The diagnosis is made by means of biochemical indicators, intact parathormone (iPTH) concentration, bone X-rays, bone densitometry and particularly bone histomorphometry. The aim of our study was to establish whether a combination of non-invasive methods can bring us closer to the diagnosis as to avoid bone biopsy.

PATIENTS AND METHODS

We chose 30 patients treated by chronic hemodialysis. Only 4 of them had no symptoms of RO. Biochemical parameters (Ca, P) and iPTH concentrations were determined. bone X-rays were taken (the parathyroid series), bone mineral density was measured by quantitative digital radiography (QDR), and bone biopsy specimens were taken for bone histomorphometry. The data were analyzed by the Statistica by StatSoft and SPSS computer programs.

RESULTS

With respect to bone histomorphometry, 10 patients had osteitis fibrosa (OF), 15 had mixed osteodystrophy (MO), 5 adynamic bone disease (ABD). There was a good correlation of iPTH and alkaline phosphatase (AP) concentrations with histomorphometric parameters. There was also a correlation between radiological changes and histomorphometric parameters. After the analysis of discrimination using the SPSS computer program, taking only iPTH into consideration, 36.6% of patients were correctly classified according to their diagnosis. Considering iPTH and densitometry, 46.6% were classified correctly. Considering iPTH and radiological changes, 60% of patients were classified correctly.

CONCLUSION

To diagnose 73.3% of patients correctly, it was necessary to consider the above mentioned non-invasive parameters, as well as AP, P, concentrations and the patient age. Histomorphometry remains the "golden standard" for diagnosing RO.

Magnesium hydrogen carbonate natural mineral water enriched with K(+)-citrate and vitamin B6 improves urinary abnormalities in patients with calcium oxalate nephrolithiasis

The influence of drinking magnesium hydrogen carbonate natural mineral water enriched with potassium citrate on urinary metabolic abnormalities was prospectively studied in 27 patients with recurrent calcium oxalate nephrolithiasis. The mean 24-hour urinary pH shifted from 6.34 to 6.93 (p < 0.01), the mean urinary magnesium/urinary creatinine ratio rose from 0.47 to 0.67 (p < 0.01), the mean urinary citrate/urinary creatinine ratio increased from 0.26 to 0.35 (p NS), and the mean 24-hour urinary calcium decreased from 7.98 to 6.05 mmol (p < 0.05). The effects of magnesium hydrogen carbonate natural mineral water enriched with potassium citrate were found to be favorable on urinary calcium, urinary magnesium/urinary creatinine ratio and urinary pH in patients with calcium oxalate nephrolithiasis.

Identification of the binding interfaces on CheY for two of its targets, the phosphatase CheZ and the flagellar switch protein fliM

CheY is the response regulator protein serving as a phosphorylation-dependent switch in the bacterial chemotaxis signal transduction pathway. CheY has a number of proteins with which it interacts during the course of the signal transduction pathway. In the phosphorylated state, it interacts strongly with the phosphatase CheZ, and also the components of the flagellar motor switch complex, specifically with FliM. Previous work has characterized peptides consisting of small regions of CheZ and FliM which interact specifically with CheY. We have quantitatively measured the binding of these peptides to both unphosphorylated and phosphorylated CheY using fluorescence spectroscopy. There is a significant enhancement of the binding of these peptides to the phosphorylated form of CheY, suggesting that these peptides share much of the binding specificity of the intact targets of the phosphorylated form of CheY. We also have used modern nuclear magnetic resonance methods to characterize the sites of interaction of these peptides on CheY. We have found that the binding sites are overlapping and primarily consist of residues in the C-terminal portion of CheY. Both peptides affect the resonances of residues at the active site, indicating that the peptides may either bind directly at the active site or exert conformational influences that reach to the active site. The binding sites for the CheZ and FliM peptides also overlap with the previously characterized CheA binding interface. These results suggest that interaction with these three proteins of the signal transduction pathway are mutually exclusive. In addition, since these three proteins are sensitive to the phosphorylation state of CheY, it may be that the C-terminal region of CheY is most sensitive for the conformational changes occurring upon phosphorylation.

Regulation of phosphatase activity in bacterial chemotaxis

Bacterial chemotaxis is the most studied model system for signaling by the widely spread family of two-component regulatory systems. It is controlled by changes in the phosphorylation level of the chemotactic response regulator, CheY, mediated by a histidine kinase (CheA) and a specific phosphatase (CheZ). While it is known that CheA activity is regulated, via the receptors, by chemotactic stimuli, the input that may regulate CheY dephosphorylation by CheZ has not been found. We measured, by using stopped-flow fluorometry, the kinetics of CheZ-mediated dephosphorylation of CheY. The onset of dephosphorylation was delayed by approximately 50 ms after mixing phosphorylated CheY (CheY approximately P) with CheZ, and a distinct overshoot was observed in the approach to the new steady state of CheY approximately P. The delay and overshoot were not observed in a hyperactive mutant CheZ protein (CheZ54RC) that does not support chemotaxis in vivo and appears to be constitutively active. CheZ activity was cooperative with respect to CheY approximately P, with a Hill-coefficient of 2.5. The observed delayed modulation of CheZ activity and its cooperativity suggest that the phosphatase activity is regulated at the level of CheY approximately P-CheZ interaction. This novel kind of interplay between a response regulator and its phosphatase may be involved in signal tuning and in adaptation to chemotactic signals.

Fungal peritonitis in patients on continuous ambulatory peritoneal dialysis

The purpose of this study was to analyze the microbiological and clinical features of fungal peritonitis in patients with endstage renal failure treated with continuous ambulatory peritoneal dialysis (CAPD). The diagnosis of peritonitis was based on abdominal discomfort or pain, cloudy peritoneal effluent with an elevated leukocyte count and isolation of fungi from the peritoneal effluent. Amphotericin B, flucytosine, ketoconazole, miconazole and more recently fluconazole were used for antifungal therapy. From 1983 to 1997 13 patients experienced 14 episodes of fungal peritonitis, comprising 3.1% of all episodes of peritonitis in the dialysis centre. Isolates from the peritoneal effluent comprised Candida tropicalis in two cases, Candida parapsilosis in two cases, Candida albicans in one case, Candida lusitaniae in one case,Cephalosporium spp. in three cases, Aspergillus fumigatus in two cases, and an Aspergillus sp., a Trichoderma sp. and a yeast in one case each. In eight cases bacterial infection shortly before the episode of fungal peritonitis was documented. In 12 (86%) cases the peritoneal catheter had to be removed. Four patients died during the treatment, and one patient died 2 months after the end of treatment due to intra-abdominal bleeding from peritoneal adhesions. Only two patients continued CAPD later; the other patients were switched to hemodialysis. It is concluded that fungal peritonitis is a rare but serious complication in CAPD patients with high rates of morbidity, mortality and drop-out from the CAPD programme (85%). The most frequent isolates were Candida spp. A predisposing factor for fungal peritonitis could be a recent bacterial infection treated with antibiotics. Early peritoneal catheter removal is recommended.

Hyperbaric oxygenation, plasma exchange, and hemodialysis for treatment of acute liver failure in a 3-year-old child

A girl aged 3 years and 4 months weighing 16 kg was treated with plasma exchange (PE), hemodialysis (HD), and hyperbaric oxygenation (HBO) for acute hepatic failure and coma. She was given a total of 13 PEs, 13 HD sessions, and 9 HBO treatments over a period of 1 month. The initial 4 PEs were followed by HD sessions while the other 8 PE treatments were given simultaneously with HD. There was no renal failure; HD was instituted to improve ammonia elimination. In 1 HD session, 20% human albumin (370 ml) was used as the dialysate to enhance bilirubin elimination. Three volumes of plasma (2,000 ml) per PE were exchanged and replaced with fresh frozen plasma (FFP). The Bellco BL 791 plasmapheresis monitor and Gambro PF1000 and PF2000 plasma filters were used. Heparin was added to prevent clotting. A dual lumen pediatric HD catheter (7 Fr) placed percutaneously into the femoral vein was used as a blood access. The Fresenius 2008 C HD monitor and the Filtral 10 dialyzer were used for HD. PE and HD were instituted simultaneously to prevent the tetanic (hypocalcemic) cramps observed with 2 previous PEs due to citrate in the FFP. The extracorporeal circuit was primed with a mixture of concentrated red cells, human albumin, and saline solution and was discarded at the end of the procedure. The average blood flow rate in PE and/or HD circuits was 80 ml/min. During HBO, the girl breathed 100% oxygen at 2.5 atm for 90 min. Throughout the treatment, the patient was in good clinical, physical, and mental condition, but she was dependent on blood purification procedures. She was referred to a liver transplant center and successfully transplanted. The etiology of liver failure has not been clarified.

The N terminus of the flagellar switch protein, FliM, is the binding domain for the chemotactic response regulator, CheY

A key event in signal transduction during chemotaxis of Salmonella typhimurium and related bacterial species is the interaction between the phosphorylated form of the response regulator CheY (CheY approximately P) and the switch of the flagellar motor, located at its base. The consequence of this interaction is a shift in the direction of flagellar rotation from the default, counterclockwise, to clockwise. The docking site of CheY approximately P at the switch is the protein FliM. The purpose of this study was to identify the CheY-binding domain of FliM. We cloned 17 fliM mutants, each defective in switching and having a point mutation at a different location, and then overexpressed and purified their products. The CheY-binding ability of each of the FliM mutant proteins was determined by chemical crosslinking. All the mutant proteins with an amino acid substitution at the N terminus, FliM6LI, FliM7SY and FliM10EG, bound CheY approximately P to a much lesser extent than did wild-type FliM. CheY approximately P-binding of the other mutant proteins was similar to wild-type FliM. To investigate whether the FliM domain that includes these three mutations is indeed the CheY-binding domain, we synthesized a peptide composed of the first 16 amino acid residues of FliM, including a highly conserved region of FliM (residues 6 to 15). The peptide bound CheY and, to a larger extent, CheY approximately P. It also competed with full-length FliM on CheY approximately P. These results indicate that the CheY-binding domain of FliM is located at the N terminus, within residues 1 to 16, and suggest that FliM monomers can form a complete site for CheY binding.

Signal termination in bacterial chemotaxis: CheZ mediates dephosphorylation of free rather than switch-bound CheY

Chemotaxis in bacteria is controlled by regulating the direction of flagellar rotation. The regulation is carried out by the chemotaxis protein CheY. When phosphorylated, CheY binds to FliM, which is one of the proteins that constitute the "gear box" (or "switch") of the flagellar motor. Consequently, the motor shifts from the default direction of rotation, counterclockwise, to clockwise rotation. This biased rotation is terminated when CheY is dephosphorylated either spontaneously or, faster, by a specific phosphatase, CheZ. Logically, one might expect CheZ to act directly on FliM-bound CheY. However, here we provide direct biochemical evidence that, in contrast to this expectation, phosphorylated CheY (CheY approximately P), bound to FliM, is protected from dephosphorylation by CheZ. The complex between CheY approximately P and FliM was trapped by cross-linking with dimethylsuberimidate, and its susceptibility to CheZ was measured. CheY approximately P complexed with FliM, unlike free CheY approximately P, was not dephosphorylated by CheZ. However, it did undergo spontaneous dephosphorylation. Nonspecific cross-linked CheY dimers, measured as a control, were dephosphorylated by CheZ. No significant binding between CheZ and any of the switch proteins was detected. It is concluded that, in the termination mechanism of signal transduction in bacterial chemotaxis, CheZ acts only on free CheY approximately P. We suggest that CheZ affects switch-bound CheY approximately P by shifting the equilibrium between bound and free CheY approximately P.

The morphology of parietal peritoneum: a scanning electron micrograph study

From 1988 to 1992, 114 patients with end-stage renal failure were treated with continuous ambulatory peritoneal dialysis (CAPD). In 30 patients (18 men, 12 women, age 31-80 years), 40 scanning electron micrographs (SEM) of parietal peritoneal tissue, obtained with biopsy, were performed: in 20 patients at the time of the first catheter implantation, in 14 patients after catheter removal (because of peritonitis in 12 patients and drainage problems in 2 patients), and in 6 patients during catheter reinsertion. In uremic patients two types of mesothelial cells were observed: hexagonal and elongated. In some patients microvilli were abundant and covered the whole surface of mesothelial cells; in other patients microvilli were lacking. Wide openings (stomata) between mesothelial cells were found in some cases, which were wider in patients with peritonitis. During peritonitis, microvilli disappeared, and mesothelial cells were covered with fibrin, leukocytes, and erythrocytes instead. In the majority of patients with peritonitis, mesothelial cells were totally peeled away, or removed, leaving a denuded surface of fibrous tissue. A recovery of the parietal peritoneum was observed in one patient at the time of peritoneal catheter reinsertion: a complete mesothelial regeneration with abundant microvilli appeared. In other patients the surface was denuded, without microvilli or mesothelial cells, covered with fibrin and fibrous tissue. Despite observed changes of the parietal peritoneum with SEM during the course of CAPD and peritonitis, changes may be reversible due to regeneration of mesothelial cells. Prolonged changes after discontinuation of peritoneal dialysis may persist in patients without mesothelial cell regeneration or with a defective process of fibrinolysis.

The treatment of staphylococcus peritonitis in patients on continuous ambulatory peritoneal dialysis

The aim of this prospective, randomized, open study was to survey the frequency course and to evaluate the therapy of peritonitis induced by staphylococci in patients on continuous ambulatory peritoneal dialysis (CAPD). From June 1983 to November 1986, 20 patients (9 men, 11 women) aged from 25 to 73 were treated. During 258 months of the CAPD treatment they had 54 episodes of peritonitis. Staphylococcus saprophyticus was the most frequent offender of peritonitis, isolated from peritoneal effluent in 44% of the cases, Staphylococcus epidermidis was isolated in 7% of the cases. Staphylococcus aureus was isolated in 5% of the cases and caused a more severe form of peritonitis. The combination of gentamicin and methicillin was used in 14 cases, in 2 cases this treatment was unsuccessful. A combination of gentamicin and cloxacillin was used in 5 cases and a combination of clindamycin and mezlocillin in 12 cases of peritonitis, giving good results in all cases. The last combination seemed to be the most effective in the treatment of staphylococcus induced peritonitis.